[Bioperl-l] Bio::Assembly::IO::bowtie circular dependency?

Mark A. Jensen maj at fortinbras.us
Tue Feb 9 16:21:21 EST 2010

Yeah, this is getting kinda hairy-- B:T:R:Samtools is
a basic wrapper for anything that wants to use
Bio::DB::Samtools ( lstein's samtools library wrapper,
a CPAN and not a BioPerl module. Savvy?). Because
its likely that other parser-like modules will want to
use samtools ( as well as wrapper-like modules), I
would vote for moving Samtools and Samtools::Config
into the bioperl-live version of Bio::Tools::Run.
(A question for another day is, should we/can we
coalesce the two instances of Bio::Tools:Run,
and where?)

----- Original Message ----- 
From: "Robert Buels" <rmb32 at cornell.edu>
To: "BioPerl List" <bioperl-l at lists.open-bio.org>; "Dan Kortschak" 
<dan.kortschak at adelaide.edu.au>
Sent: Tuesday, February 09, 2010 3:27 PM
Subject: [Bioperl-l] Bio::Assembly::IO::bowtie circular dependency?

> Bio::Assembly::IO::bowtie uses Bio::Tools::Run::Samtools, which is part of 
> bioperl-run.  Doesn't that introduce a circular dependency between 
> bioperl-live and bioperl-run?
> Perhaps it should be split out into its own CPAN distribution that depends on 
> both bioperl-run and bioperl-live?  Or maybe some way can be found for it to 
> not use Bio::Tools::Run::Samtools?
> Rob
> -- 
> Robert Buels
> Bioinformatics Analyst, Sol Genomics Network
> Boyce Thompson Institute for Plant Research
> Tower Rd
> Ithaca, NY  14853
> Tel: 503-889-8539
> rmb32 at cornell.edu
> http://www.sgn.cornell.edu
> _______________________________________________
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> Bioperl-l at lists.open-bio.org
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